To understand the behavior of trace metals in the salt marsh at Skallingen, Danish Wadden Sea, we investigated a profile from surface to 25 cm depth of the salt marsh sediment, focusing primarily on clay mineralogy and grain size distribution of the sediments and their relationship with trace metals. The clay assembly of the sediment consists of illite, kaolinite and much less chlorite and smectite. The major clay minerals of illite, kaolinite as well as chlorite correlate very poorly with all the trace metals investigated, due probably to the weak competing strength of these clays compared with the other adsorbents and to low availability of the mobile trace metals in the system. Correlation between trace metals and clay minerals may therefore be used as an indicator in environmental assessment. Fine grain fractions of the sediment increased markedly after salt marsh invasion in about 1931 but decreased after 1964. This increase was contributed mainly by the grains finer than 20 µm while the fraction of 40–63 µm actually decreased soon after the invasion. The relation between most of the trace metals and grain size distributions is close in general but far from linear. The drastic turning point is observed at about 30 µm, around where the correlation coefficient r drops from 0.8 to 0.1. Adsorption is the controlling mechanism for the behavior of trace metals in the salt marsh. Fe/Mn (hydr)oxides and organic matter play the key role.